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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:23, 17 September 2013


Full id: C460_Neutrophils_corpus_thalamus_substantia_parietal_globus_locus



Phase1 CAGE Peaks

Hg19::chr10:1278750..1278767,-p@chr10:1278750..1278767
-
Hg19::chr10:1282470..1282519,-p3@ADARB2
Hg19::chr11:78049190..78049232,-p@chr11:78049190..78049232
-
Hg19::chr2:71804278..71804331,+p@chr2:71804278..71804331
+
Hg19::chr4:185729602..185729613,-p15@ACSL1
Hg19::chr9:91985133..91985173,-p@chr9:91985133..91985173
-
Hg19::chr9:91985218..91985232,-p@chr9:91985218..91985232
-
Hg19::chr9:91985236..91985347,-p@chr9:91985236..91985347
-
Hg19::chr9:91985398..91985439,-p@chr9:91985398..91985439
-
Hg19::chr9:91985441..91985477,-p@chr9:91985441..91985477
-
Hg19::chr9:91985535..91985584,-p@chr9:91985535..91985584
-
Hg19::chr9:91985611..91985646,-p@chr9:91985611..91985646
-
Hg19::chr9:91985687..91985700,-p@chr9:91985687..91985700
-
Hg19::chr9:91985741..91985765,-p@chr9:91985741..91985765
-
Hg19::chr9:91985867..91985882,-p@chr9:91985867..91985882
-
Hg19::chr9:91985883..91985947,-p@chr9:91985883..91985947
-
Hg19::chr9:91986315..91986327,-p@chr9:91986315..91986327
-
Hg19::chr9:91987177..91987203,-p@chr9:91987177..91987203
-
Hg19::chr9:91987221..91987232,-p@chr9:91987221..91987232
-
Hg19::chr9:91987337..91987359,-p@chr9:91987337..91987359
-
Hg19::chr9:91987399..91987413,-p@chr9:91987399..91987413
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0202658856665421
GO:0015645fatty-acid ligase activity0.0202658856665421
GO:0004000adenosine deaminase activity0.0202658856665421
GO:0003727single-stranded RNA binding0.0202658856665421
GO:0016877ligase activity, forming carbon-sulfur bonds0.0202658856665421
GO:0019239deaminase activity0.0202658856665421
GO:0031903microbody membrane0.0202658856665421
GO:0005778peroxisomal membrane0.0202658856665421
GO:0044439peroxisomal part0.0202658856665421
GO:0044438microbody part0.0202658856665421
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0202658856665421
GO:0003725double-stranded RNA binding0.0202658856665421
GO:0005741mitochondrial outer membrane0.0254740322863236
GO:0031968organelle outer membrane0.0254740322863236
GO:0007586digestion0.0254740322863236
GO:0019867outer membrane0.0254740322863236
GO:0042579microbody0.0254740322863236
GO:0005777peroxisome0.0254740322863236
GO:0005792microsome0.0387065963269252
GO:0042598vesicular fraction0.0387065963269252
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0397555679538304
GO:0006631fatty acid metabolic process0.0397555679538304



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube1.05e-4356
neural rod1.05e-4356
future spinal cord1.05e-4356
neural keel1.05e-4356
regional part of nervous system2.74e-4053
regional part of brain2.74e-4053
adult organism7.31e-36114
regional part of forebrain1.09e-3541
forebrain1.09e-3541
anterior neural tube1.09e-3541
future forebrain1.09e-3541
brain7.83e-3468
future brain7.83e-3468
central nervous system7.68e-3381
nervous system2.27e-3189
neural plate3.19e-2982
presumptive neural plate3.19e-2982
brain grey matter3.19e-2834
gray matter3.19e-2834
telencephalon3.54e-2834
neurectoderm3.59e-2886
regional part of telencephalon7.04e-2632
cerebral hemisphere1.11e-2532
pre-chordal neural plate1.79e-2361
regional part of cerebral cortex1.30e-2122
neocortex2.10e-1920
ecto-epithelium3.43e-19104
cerebral cortex3.34e-1825
pallium3.34e-1825
structure with developmental contribution from neural crest5.59e-15132
basal ganglion5.87e-129
nuclear complex of neuraxis5.87e-129
aggregate regional part of brain5.87e-129
collection of basal ganglia5.87e-129
cerebral subcortex5.87e-129
neural nucleus6.49e-129
nucleus of brain6.49e-129
ectoderm-derived structure2.56e-10171
ectoderm2.56e-10171
presumptive ectoderm2.56e-10171
telencephalic nucleus1.55e-097
posterior neural tube2.89e-0915
chordal neural plate2.89e-0915
diencephalon5.38e-097
future diencephalon5.38e-097
brainstem1.02e-086
organ system subdivision1.43e-08223
gyrus4.26e-086
limbic system2.03e-075
segmental subdivision of nervous system2.53e-0713
parietal lobe4.60e-075
temporal lobe9.55e-076


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.14.3196e-05
MA0004.10.169125
MA0006.10.559101
MA0007.10.156885
MA0009.10.543169
MA0014.10.00441763
MA0017.10.31911
MA0019.10.757112
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.10.24162
MA0040.10.472301
MA0041.10.181587
MA0042.10.483482
MA0043.10.543454
MA0046.10.533373
MA0048.10.098451
MA0050.10.160894
MA0051.10.238478
MA0052.10.475699
MA0055.10.00257143
MA0056.10
MA0057.10.0306551
MA0058.10.35609
MA0059.12.35007
MA0060.10.0296044
MA0061.10.0956181
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.126.589
MA0069.10.529912
MA0070.10.519883
MA0071.10.213282
MA0072.10.515863
MA0073.1997.763
MA0074.10.23792
MA0076.10.119431
MA0077.10.508982
MA0078.10.31524
MA0081.10.109654
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.179504
MA0089.10
MA0090.10.127987
MA0091.10.170864
MA0092.11.41571
MA0093.10.268179
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.0794742
MA0103.10.0719484
MA0105.10.0246233
MA0106.10.272934
MA0107.10.177872
MA0108.20.398967
MA0109.10
MA0111.10.136202
MA0113.10.285689
MA0114.10.388646
MA0115.10.766188
MA0116.10.0483327
MA0117.10.577217
MA0119.10.100647
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.10.018888
MA0140.10.211376
MA0141.10.108582
MA0142.10.978356
MA0143.12.17851
MA0144.10.155387
MA0145.10.00212809
MA0146.10.000121402
MA0147.10.186237
MA0148.10.546085
MA0149.10.204488
MA0062.20.0205944
MA0035.20.210872
MA0039.232.3096
MA0138.20.316226
MA0002.22.57387
MA0137.20.295276
MA0104.20.0293723
MA0047.20.728835
MA0112.20.00179367
MA0065.20.220145
MA0150.11.2794
MA0151.10
MA0152.10.216094
MA0153.10.633172
MA0154.10.00405158
MA0155.13.10207
MA0156.10.0888107
MA0157.10.352016
MA0158.10
MA0159.10.187008
MA0160.10.196462
MA0161.10
MA0162.10.783827
MA0163.12.34402e-05
MA0164.10.801488
MA0080.20.0778984
MA0018.20.274004
MA0099.20.216352
MA0079.20.00024089
MA0102.21.05522
MA0258.10.0364681
MA0259.10.0531061
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
MYC#460992.238120802118320.01085033261059840.0400126368249105
SUZ12#2351249.545863030678650.000721851695086120.00576592498532309



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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